Readings with further information

• Bryan. 2018. Excuse Me, Do You Have a Moment to Talk About Version Control? The American Statistician, 72(1), 20-27. https://doi.org/10.1080/00031305.2017.1399928
• Turner et al. 2020. Open Code and Software: a Primer from UKRN. https://doi.org/10.31219/osf.io/qw9ck
• Git and GitHub for R. https://happygitwithr.com/
• Brailey. 2022. Using GitHub and Rstudio. https://osf.io/dgw2s/

Why GitHub? The analogy of climbing

Source: illustrations by @allison_horst

Git

• Who has used Git previously? What for?
• Who has used any kind of version control previously?

Git as Version Control

You all have used version control previously:

• “Save early, save often”.
• Easiest version control: the back-button.
• “Track-changes” in MS Word is a rudimentary form of version control.

Git is a sophisticated form of version control. Git…

• … maintains a single, updated version of each file.
• … keeps a record of all previous versions.
• … keeps a record of exact changes between the versions.
• … collaborators can work simultaneously.
• … documents who made changes, when and why.

Why should I learn yet another tool? Git as Version Control

• Maintain an overview
• Access previous versions

• Strengthen Collaboration
• Foster Transparency

• Next:
• Create an academic website
• Create an academic CV
• → Qmd and Rmd allow us to use the same document for both

Git: a preview

Why Git? 1) Streamline your work

Source: illustrations by @allison_horst

Why Git? 2) Support others and yourself

Source: illustrations by @allison_horst

Why Git? 3) Reuse your work

Source: illustrations by @allison_horst

Why Git? 4) Contribute earlier

Source: illustrations by @allison_horst

Why Git? 5) Fail safely

Source: illustrations by @allison_horst

Why Git? Summary

1. Streamline your work
2. Support others and yourself
3. Reuse your work
4. Contribute earlier
5. Fail safely

To recap at home

• What is a … ?
  • Repository
  • Branch
  • Pull request
  • work flow using Git

Simulation to learn using basic Git commands

Git basics

Generally, git operates through a shell. (Later on, we will install a GUI can make life easier.)

What is a shell?

Git: Terminiology (3): what’s the difference?

Git: Terminiology (3): tools

Git is the command line version control system (VCS) software, which works on your local computer.

GitHub is an internet hosting service for git repositories.

GitHub Desktop is an application that enables you to interact with GitHub using a GUI instead of the command line or a web browser.

GitHub Desktop: Getting started

• Install and use GitHub Desktop (especially for beginners)

GitHub Desktop: track version history

Using GitHub and Rstudio integrated

## Pro Tip

• Sign up for a free GitHub Pro account if you are a student or a free GitHub Team account if you are a teacher.

Common mistake

• You don’t remember whether you have Git installed previously.

• Solution: You may be able to find Git using which git (in a bash shell) or where git (in a Windows shell)

My two cents 💰

• Do not create a Git repo inside your Git repo

• Git repos are not supposed to go into Google Drive, DropBox, or OneDrive, but…

Additional Tipps

# new branch
git checkout -b new_branch_name
# checkout existing branch
git checkout existing_branch_name
# reset file to a previous version
git checkout b68cb2dc1a53275dd779391bcac96a96c559b894 -- file_name.md

Publishing Code

Sharing code publicly can be very useful but poses some challenges. To avoid security issues or problems for you and other users consider the following tipps.

Publishing Code > Security

Start a new git repository and copy paste your code when you publish. You might have information in your git history you don’t want to share (passwords, private access tokens, “unprofessional” text or code from the early days of a project)

Publishing Code > README.md

Add a “Usage” and “Contributing” section to your README.md

• Add a sentence or two on the WHY of the project
• Add a section “Usage” on how to install/use your project
• Have a simple and short code example showcasing how to use the project
• Explain the basic project structure

Get started on GitHub

Collaboration in teams

How to collaborate? Two common workflows

1. Shared repo workflow

• For small projects where you are basically in the same physical space (e.g. lab with offices near each other).
• Be careful! You are cloning the main repository.
• Everyone has push and pull access to the central repo, so be careful and:
  • Never commit to the master directly.
  • Always do your work on a different branch from master.

2. Fork and pull workflow

• This model is used by larger teams.
• The “owner”/“Project Leader” of the upstream repo assigns rights to “Collaborators”.
• Collaborators do not have push access to main (upstream) repo.
• Project Lead accepts Pull Requests (PRs) fro collaborators, reviews them, then merges them into main repo.

1) Shared repo workflow

2) Fork and pull workflow

Merging branches

Two common errors

• Push rejected. This can happen if you have changes on the remote and on your local repo. > - Solution: Pull first. Resolve the conflict. Then try your push again.

• fatal: not a git repository. The command cannot be executed because the current directory is not a Git directory. > - Solution: initialize the repo or change directory to the repo

Some advice before we practice

• Commit early and often.

• Push to your remote on GitHub often (but not as often as you commit).

• Establish a naming convention for commits.

• Use tags to mark key steps.

• Fork and clone from foreign repos (instead of “just cloning”)

• Branch of your development version, especially in teams.

Now it’s your turn: use the power of Git

Source: illustrations by @allison_horst

Working with GitHub